234D image
Deposition Date 1995-06-22
Release Date 1996-01-31
Last Version Date 2024-02-14
Entry Detail
PDB ID:
234D
Keywords:
Title:
CRYSTAL STRUCTURE OF FOUR MORPHOLINO-DOXORUBICIN ANTICANCER DRUGS COMPLEXED WITH D(CGTACG) AND D(CGATCG): IMPLICATIONS IN DRUG-DNA CROSSLINK
Biological Source:
Source Organism:
(Taxon ID: ) (Taxon ID: )
Method Details:
Experimental Method:
Resolution:
1.80 Å
R-Value Observed:
0.19
Space Group:
P 41 21 2
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
Chain IDs:A
Chain Length:6
Number of Molecules:1
Biological Source:
Ligand Molecules
Primary Citation
Crystal structures of four morpholino-doxorubicin anticancer drugs complexed with d(CGTACG) and d(CGATCG): implications in drug-DNA crosslink.
J.Biomol.Struct.Dyn. 13 103 117 (1995)
PMID: 8527023

Abstact

Among the new generations of anthracycline drugs, morpholino-doxorubicin (MDox) and its derivative have unusually potent activity when compared with the parent doxorubicin. 3"-Cyano-morpholino-doxorubicin (CN-MDox) has been suggested to form a covalent crosslink to DNA, although the exact mode of interactions remains unclear. To establish the structural basis of this crosslink, we carried out X-ray diffraction analyses of the complexes between four different morpholino-doxorubicins (i.e., MDox, CN-MDox, (R)- and (S)-2"-methoxy-morpholino-Dox (MMDox)) and two DNA hexamers CGTACG and CGATCG. Their crystal data are similar to other Dau/Dox complexes with space group P4(1)2(1)2,a = b approximately 28 A, c approximately 53 A. The refined structures at approximately 1.8 A resolution revealed that two drug molecules bind to the duplex with the aglycons intercalated between the CpG steps with their N3'-morpholino-daunosamines in the minor groove. The morpholino moiety is flexible and may adopt different conformations dependent on the sequence context. The O1" atoms of the two morpholino groups in the drug-DNA complexes are in van der Waals contact. The structural results suggest possible crosslinking mechanism of CN-MDox. It is worth pointing out that by linking two piperazinyl- or piperidinyl-doxorubicins at the 1" positions a new type of bis-doxorubicin derivatives may be synthesized which may bind to a hexanucleotide sequence with some specificity.

Legend

Protein

Chemical

Disease

Primary Citation of related structures